--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/core/parsing/GtfParser.py	Fri Jan 18 04:54:14 2013 -0500
@@ -0,0 +1,113 @@
+#
+# Copyright INRA-URGI 2009-2010
+# 
+# This software is governed by the CeCILL license under French law and
+# abiding by the rules of distribution of free software. You can use,
+# modify and/ or redistribute the software under the terms of the CeCILL
+# license as circulated by CEA, CNRS and INRIA at the following URL
+# "http://www.cecill.info".
+# 
+# As a counterpart to the access to the source code and rights to copy,
+# modify and redistribute granted by the license, users are provided only
+# with a limited warranty and the software's author, the holder of the
+# economic rights, and the successive licensors have only limited
+# liability.
+# 
+# In this respect, the user's attention is drawn to the risks associated
+# with loading, using, modifying and/or developing or reproducing the
+# software by the user in light of its specific status of free software,
+# that may mean that it is complicated to manipulate, and that also
+# therefore means that it is reserved for developers and experienced
+# professionals having in-depth computer knowledge. Users are therefore
+# encouraged to load and test the software's suitability as regards their
+# requirements in conditions enabling the security of their systems and/or
+# data to be ensured and, more generally, to use and operate it in the
+# same conditions as regards security.
+# 
+# The fact that you are presently reading this means that you have had
+# knowledge of the CeCILL license and that you accept its terms.
+#
+import re
+import sys
+from SMART.Java.Python.structure.Interval import Interval
+from SMART.Java.Python.structure.Transcript import Transcript
+from commons.core.parsing.TranscriptListParser import TranscriptListParser
+
+
+class GtfParser(TranscriptListParser):
+    """A class that parses a GTF file and create a transcript list"""
+
+
+    def __init__(self, fileName, verbosity = 0):
+        super(GtfParser, self).__init__(fileName, verbosity)
+
+
+    def __del__(self):
+        super(GtfParser, self).__del__()
+
+
+    def getFileFormats():
+        return ["gtf", "gtf2"]
+    getFileFormats = staticmethod(getFileFormats)
+
+
+    def skipFirstLines(self):
+        pass
+
+
+    def parseLine(self, line):
+        if line[0] == "#":
+            return None
+        m = re.search(r"^\s*(\S+)\s+(\S+)\s+(\S+)\s+(\d+)\s+(\d+)\s+(\S+)\s+([+-.])\s+(\S+)\s+(\S.*)$", line)
+        if m == None:
+            raise Exception("\nLine %d '%s' does not have a GTF format\n" % (self.currentLineNb, line))
+        interval = Interval()
+        interval.setChromosome(m.group(1))
+        interval.setName("unnamed transcript")
+        interval.setStart(min(int(m.group(4)), int(m.group(5))))
+        interval.setEnd(max(int(m.group(4)), int(m.group(5))))
+        if m.group(7) == ".":
+            interval.setDirection("+")
+        else:
+            interval.setDirection(m.group(7))
+        if m.group(6).isdigit():
+            interval.setTagValue("score", m.group(6))
+        type = m.group(3)
+
+        if type not in ("transcript", "exon"):
+            return None
+
+        remainings = m.group(9).split(";")
+        for remaining in remainings:
+            remaining = remaining.strip()
+            if remaining == "":
+                continue
+            parts = remaining.split(" ", 1)
+            field = parts[0].strip()
+            value = " ".join(parts[1:]).strip(" \"")
+            if field == "transcript_id":
+                interval.setTagValue("ID", value)
+            elif field == "gene_name":
+                interval.setName(value)
+            elif field == "transcript_name":
+                interval.setName(value)
+            elif field == "exon_number":
+                continue
+            else:
+                try:
+                    intValue = int(value)
+                    interval.setTagValue(field, intValue)
+                except ValueError:
+                    interval.setTagValue(field, value)
+
+        self.currentTranscriptAddress = self.previousTranscriptAddress
+        if self.currentTranscript == None or interval.getTagValue("ID") != self.currentTranscript.getTagValue("ID"):
+            transcript = self.currentTranscript
+            self.currentTranscript = Transcript()
+            self.currentTranscript.copy(interval)
+            self.currentTranscript.setTagValue("feature", "transcript")
+            self.previousTranscriptAddress = self.currentAddress
+            return transcript
+        if type == "exon":
+            self.currentTranscript.addExon(interval)
+        return None